VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Wed Jun 02 2010 - 11:35:57 CDT

Dear John

Thanks for reply.

Sorry for not expalining the question properly.

I have used Desmond for my simulation and for analysis i'm using VMD.

I have tried to run the plug-in after loading the complex with trajectories.

However it failed to assume the dafault parameter file (.psf)

I can able to generate xsc file.

Kindly advice.

Many Thanks
Balaji

On Wed, Jun 2, 2010 at 5:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> You can either do this with the "NAMDEnergy" plugin, or by running
> NAMD manually with the right config file etc:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 02, 2010 at 01:29:38PM +0100, ban arn wrote:
> > Hi All,
> >
> > I would like to calculate interaction energy of protein and ligand
> over
> > trajectories.
> >
> > Can anyone suggest me is there any script available for doing the same
> in
> > VMD.
> >
> > Many Thanks
> > Balaji
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>